diff options
Diffstat (limited to 'src/Persistence_representations/utilities/persistence_heat_maps')
11 files changed, 763 insertions, 0 deletions
diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt new file mode 100644 index 00000000..0dd63852 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/CMakeLists.txt @@ -0,0 +1,63 @@ +cmake_minimum_required(VERSION 2.6) +project(Persistence_representations_heat_maps_utilities) + +file(COPY "${CMAKE_SOURCE_DIR}/data/persistence_diagram/simple_diagram.txt" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/") + +add_executable ( create_persistence_heat_maps create_persistence_heat_maps.cpp ) +target_link_libraries(create_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_persistence_heat_maps COMMAND $<TARGET_FILE:create_persistence_heat_maps> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + + +add_executable ( create_pssk create_pssk.cpp ) +target_link_libraries(create_pssk ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_pssk COMMAND $<TARGET_FILE:create_pssk> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( create_p_h_m_weighted_by_distance_from_diagonal create_p_h_m_weighted_by_distance_from_diagonal.cpp ) +target_link_libraries(create_p_h_m_weighted_by_distance_from_diagonal ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_p_h_m_weighted_by_distance_from_diagonal COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_distance_from_diagonal> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( create_p_h_m_weighted_by_squared_diag_distance create_p_h_m_weighted_by_squared_diag_distance.cpp ) +target_link_libraries(create_p_h_m_weighted_by_squared_diag_distance ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_p_h_m_weighted_by_squared_diag_distance COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_squared_diag_distance> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( create_p_h_m_weighted_by_arctan_of_their_persistence create_p_h_m_weighted_by_arctan_of_their_persistence.cpp ) +target_link_libraries(create_p_h_m_weighted_by_arctan_of_their_persistence ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME create_p_h_m_weighted_by_arctan_of_their_persistence COMMAND $<TARGET_FILE:create_p_h_m_weighted_by_arctan_of_their_persistence> + "10" "-1" "-1" "4" "-1" "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( average_persistence_heat_maps average_persistence_heat_maps.cpp ) +target_link_libraries(average_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME average_persistence_heat_maps COMMAND $<TARGET_FILE:average_persistence_heat_maps> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( plot_persistence_heat_map plot_persistence_heat_map.cpp ) +target_link_libraries(plot_persistence_heat_map ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME plot_persistence_heat_map COMMAND $<TARGET_FILE:plot_persistence_heat_map> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( compute_distance_of_persistence_heat_maps compute_distance_of_persistence_heat_maps.cpp ) +target_link_libraries(compute_distance_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_distance_of_persistence_heat_maps COMMAND $<TARGET_FILE:compute_distance_of_persistence_heat_maps> + "1" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") + +add_executable ( compute_scalar_product_of_persistence_heat_maps compute_scalar_product_of_persistence_heat_maps.cpp ) +target_link_libraries(compute_scalar_product_of_persistence_heat_maps ${Boost_SYSTEM_LIBRARY}) + +add_test(NAME compute_scalar_product_of_persistence_heat_maps COMMAND $<TARGET_FILE:compute_scalar_product_of_persistence_heat_maps> + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt" + "${CMAKE_CURRENT_BINARY_DIR}/simple_diagram.txt") diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp new file mode 100644 index 00000000..4e81375a --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/average_persistence_heat_maps.cpp @@ -0,0 +1,65 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_heat_maps.h> + +#include <iostream> +#include <vector> + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; + +int main(int argc, char** argv) { + std::cout << "This program computes average persistence landscape of persistence landscapes created based on " + "persistence diagrams provided as an input. Please call this program with the names of files with " + "persistence diagrams \n"; + std::vector<const char*> filenames; + + if (argc == 1) { + std::cout << "No input files given, the program will now terminate \n"; + return 1; + } + + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence landscapes...\n"; + std::vector<Persistence_heat_maps*> maps; + for (size_t i = 0; i != filenames.size(); ++i) { + Persistence_heat_maps* l = new Persistence_heat_maps; + l->load_from_file(filenames[i]); + maps.push_back(l); + } + + Persistence_heat_maps av; + av.compute_average(maps); + + av.print_to_file("average.mps"); + + for (size_t i = 0; i != filenames.size(); ++i) { + delete maps[i]; + } + + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp new file mode 100644 index 00000000..befb0837 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_distance_of_persistence_heat_maps.cpp @@ -0,0 +1,93 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; + +int main(int argc, char** argv) { + std::cout << "This program computes distance of persistence heat maps stored in a file (the file needs to be created " + "beforehand). \n"; + std::cout << "The first parameter of a program is an integer p. The program compute L^p distance of the two heat " + "maps. For L^infty distance choose p = -1. \n"; + std::cout << "The remaining parameters of this program are names of files with persistence heat maps.\n"; + + if (argc < 3) { + std::cout << "Wrong number of parameters, the program will now terminate \n"; + return 1; + } + + int pp = atoi(argv[1]); + double p = std::numeric_limits<double>::max(); + if (pp != -1) { + p = pp; + } + + std::vector<const char*> filenames; + for (int i = 2; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector<Persistence_heat_maps> maps; + maps.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + Persistence_heat_maps l; + l.load_from_file(filenames[file_no]); + maps.push_back(l); + } + + // and now we will compute the scalar product of landscapes. + + // first we prepare an array: + std::vector<std::vector<double> > distance(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector<double> v(filenames.size(), 0); + distance[i] = v; + } + + // and now we can compute the distances: + for (size_t i = 0; i != filenames.size(); ++i) { + for (size_t j = i; j != filenames.size(); ++j) { + distance[i][j] = distance[j][i] = maps[i].distance(maps[j], p); + } + } + + // and now output the result to the screen and a file: + std::ofstream out; + out.open("distance"); + for (size_t i = 0; i != distance.size(); ++i) { + for (size_t j = 0; j != distance.size(); ++j) { + std::cout << distance[i][j] << " "; + out << distance[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp new file mode 100644 index 00000000..c684a336 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/compute_scalar_product_of_persistence_heat_maps.cpp @@ -0,0 +1,79 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <vector> + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; + +int main(int argc, char** argv) { + std::cout << "This program computes scalar product of persistence landscapes stored in a file (the file needs to be " + "created beforehand). \n"; + std::cout << "The parameters of this programs are names of files with persistence landscapes.\n"; + + std::vector<const char*> filenames; + for (int i = 1; i < argc; ++i) { + filenames.push_back(argv[i]); + } + std::vector<Persistence_heat_maps> maps; + maps.reserve(filenames.size()); + for (size_t file_no = 0; file_no != filenames.size(); ++file_no) { + Persistence_heat_maps l; + l.load_from_file(filenames[file_no]); + maps.push_back(l); + } + + // and now we will compute the scalar product of landscapes. + + // first we prepare an array: + std::vector<std::vector<double> > scalar_product(filenames.size()); + for (size_t i = 0; i != filenames.size(); ++i) { + std::vector<double> v(filenames.size(), 0); + scalar_product[i] = v; + } + + // and now we can compute the scalar product: + for (size_t i = 0; i != maps.size(); ++i) { + for (size_t j = i; j != maps.size(); ++j) { + scalar_product[i][j] = scalar_product[j][i] = maps[i].compute_scalar_product(maps[j]); + } + } + + // and now output the result to the screen and a file: + std::ofstream out; + out.open("scalar_product"); + for (size_t i = 0; i != scalar_product.size(); ++i) { + for (size_t j = 0; j != scalar_product.size(); ++j) { + std::cout << scalar_product[i][j] << " "; + out << scalar_product[i][j] << " "; + } + std::cout << std::endl; + out << std::endl; + } + out.close(); + + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp new file mode 100644 index 00000000..2bf185a3 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_arctan_of_their_persistence.cpp @@ -0,0 +1,84 @@ +/* This file is part of the Gudhi Library. The Gudhi library +* (Geometric Understanding in Higher Dimensions) is a generic C++ +* library for computational topology. +* +* Author(s): Pawel Dlotko +* +* Copyright (C) 2016 INRIA (France) +* +* This program is free software: you can redistribute it and/or modify +* it under the terms of the GNU General Public License as published by +* the Free Software Foundation, either version 3 of the License, or +* (at your option) any later version. +* +* This program is distributed in the hope that it will be useful, +* but WITHOUT ANY WARRANTY; without even the implied warranty of +* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +* GNU General Public License for more details. +* +* You should have received a copy of the GNU General Public License +* along with this program. If not, see <http://www.gnu.org/licenses/>. +*/ + +#include <gudhi/Persistence_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using arc_tan_of_persistence_of_point = Gudhi::Persistence_representations::arc_tan_of_persistence_of_point; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps<arc_tan_of_persistence_of_point>; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " + "weighted by the arc tangential of their persistence.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + "based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 5) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi(argv[1]); + double min_ = atof(argv[2]); + double max_ = atof(argv[3]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp new file mode 100644 index 00000000..ec9477f1 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_distance_from_diagonal.cpp @@ -0,0 +1,84 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using distance_from_diagonal_scaling = Gudhi::Persistence_representations::distance_from_diagonal_scaling; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps<distance_from_diagonal_scaling>; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " + "weighted by the distance of a center from the diagonal.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + "based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 5) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi(argv[1]); + double min_ = atof(argv[2]); + double max_ = atof(argv[3]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 6; i != argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp new file mode 100644 index 00000000..ffec8b3d --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_p_h_m_weighted_by_squared_diag_distance.cpp @@ -0,0 +1,85 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using squared_distance_from_diagonal_scaling = + Gudhi::Persistence_representations::squared_distance_from_diagonal_scaling; +using Persistence_heat_maps = + Gudhi::Persistence_representations::Persistence_heat_maps<squared_distance_from_diagonal_scaling>; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence heat map of diagrams provided as an input. The Gaussian kernels are " + "weighted by the square of distance of a center from the diagonal.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + "based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 5) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi(argv[1]); + double min_ = atof(argv[2]); + double max_ = atof(argv[3]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp new file mode 100644 index 00000000..db2f0008 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_persistence_heat_maps.cpp @@ -0,0 +1,80 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_heat_maps.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; + +int main(int argc, char** argv) { + std::cout << "This program creates persistence heat map of diagrams provided as an input.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + "based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If your input file contains persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + if (argc < 5) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + size_t size_of_grid = (size_t)atoi(argv[1]); + double min_ = atof(argv[2]); + double max_ = atof(argv[3]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + std::vector<const char*> filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + Persistence_heat_maps l(filenames[i], filter, false, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".mps"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp new file mode 100644 index 00000000..6aefbb00 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/create_pssk.cpp @@ -0,0 +1,81 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/PSSK.h> + +#include <iostream> +#include <sstream> +#include <limits> +#include <vector> + +using PSSK = Gudhi::Persistence_representations::PSSK; + +int main(int argc, char** argv) { + std::cout << "This program creates PSSK of diagrams provided as an input.\n"; + std::cout << "The first parameter of a program is an integer, a size of a grid.\n"; + std::cout << "The second and third parameters are min and max of the grid. If you want those numbers to be computed " + "based on the data, set them both to -1 \n"; + std::cerr << "The fourth parameter is an integer, the standard deviation of a Gaussian kernel expressed in a number " + "of pixels \n"; + std::cout << "The fifth parameter of this program is a dimension of persistence that will be used in creation of the " + "persistence heat maps."; + std::cout << "If our input files contain persistence pairs of various dimension, as a fifth parameter of the " + "procedure please provide the dimension of persistence you want to use."; + std::cout << "If in your file there are only birth-death pairs of the same dimension, set the first parameter to -1." + << std::endl; + std::cout << "The remaining parameters are the names of files with persistence diagrams. \n"; + + if (argc < 5) { + std::cout << "Wrong parameter list, the program will now terminate \n"; + return 1; + } + + size_t size_of_grid = (size_t)atoi(argv[1]); + double min_ = atof(argv[2]); + double max_ = atof(argv[3]); + size_t stdiv = atof(argv[4]); + + unsigned dimension = std::numeric_limits<unsigned>::max(); + int dim = atoi(argv[5]); + if (dim >= 0) { + dimension = (unsigned)dim; + } + + std::vector<const char*> filenames; + for (int i = 6; i < argc; ++i) { + filenames.push_back(argv[i]); + } + + std::cout << "Creating persistence heat maps...\n"; + std::vector<std::vector<double> > filter = Gudhi::Persistence_representations::create_Gaussian_filter(stdiv, 1); + + for (size_t i = 0; i != filenames.size(); ++i) { + std::cout << "Creating a heat map based on a file : " << filenames[i] << std::endl; + PSSK l(filenames[i], filter, size_of_grid, min_, max_, dimension); + + std::stringstream ss; + ss << filenames[i] << ".pssk"; + l.print_to_file(ss.str().c_str()); + } + std::cout << "Done \n"; + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp new file mode 100644 index 00000000..a7c9f2d8 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/plot_persistence_heat_map.cpp @@ -0,0 +1,38 @@ +/* This file is part of the Gudhi Library. The Gudhi library + * (Geometric Understanding in Higher Dimensions) is a generic C++ + * library for computational topology. + * + * Author(s): Pawel Dlotko + * + * Copyright (C) 2016 INRIA (France) + * + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as published by + * the Free Software Foundation, either version 3 of the License, or + * (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program. If not, see <http://www.gnu.org/licenses/>. + */ + +#include <gudhi/Persistence_heat_maps.h> + +#include <iostream> +#include <sstream> + +using constant_scaling_function = Gudhi::Persistence_representations::constant_scaling_function; +using Persistence_heat_maps = Gudhi::Persistence_representations::Persistence_heat_maps<constant_scaling_function>; + +int main(int argc, char** argv) { + std::cout << "This program plot persistence landscape stored in a file (the file needs to be created beforehand). " + "Please call the code with the name of a landscape file \n"; + Persistence_heat_maps l; + l.load_from_file(argv[1]); + l.plot(argv[1]); + return 0; +} diff --git a/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps b/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps new file mode 100644 index 00000000..b7643887 --- /dev/null +++ b/src/Persistence_representations/utilities/persistence_heat_maps/simple_diagram.txt.mps @@ -0,0 +1,11 @@ +0.93 8.0707 +0.0492104 0.03889 0.0190956 0.00603584 0.00131569 0.000120934 2.10152e-05 0 0 0 +0.0650745 0.0539306 0.0296488 0.011745 0.00357642 0.000695928 0.000120934 0 0 0 +0.0572665 0.0559446 0.0409942 0.0230905 0.00937173 0.00242903 0.000422102 0 0 0 +0.0409942 0.0559656 0.0573874 0.0408475 0.0192639 0.00628964 0.00178718 0.000422102 0.000120934 2.10152e-05 +0.0296488 0.0540515 0.0657704 0.0519133 0.0283092 0.0132056 0.00628964 0.00242903 0.000695928 0.000120934 +0.0190956 0.0393121 0.0516395 0.0465955 0.0359385 0.0283092 0.0192639 0.00937173 0.00357642 0.00131569 +0.00847814 0.0188418 0.0281882 0.0358964 0.0465955 0.0519133 0.0408475 0.0230905 0.011745 0.00603584 +0.00242903 0.00628964 0.0132056 0.0281882 0.0516395 0.0657704 0.0573874 0.0409942 0.0296488 0.0190956 +0.000422102 0.00178718 0.00628964 0.0188418 0.0393121 0.0540515 0.0559656 0.0559446 0.0539306 0.03889 +0 0.000422102 0.00242903 0.00847814 0.0190956 0.0296488 0.0409942 0.0572665 0.0650745 0.0492104 |